9.2 Methods
9.2.16 Meta-Analysis of RNAseq Data from adult mouse microglia
Meta-analysis of published RNAseq data from adult mouse microglia at different ages was carried out using the GREP2 pipeline with the web-platform GREIN and the R pack-agesedgeRandorg.Mm.eg.db. For the selection of RNAseq data the web-platform GREIN was used, that offers processed RNAseq data from the genomics data repository GEO.
The database was searched for experiments performed in Mus musculus and the key-word "microglia". Each GSE search result was screened for the availability of untreated microglia control samples. A detailed list of included studies (GSE, n = 18) and individ-ual samples (GSM, n= 132) and their source animals is given in the Appendix 10.5.
Raw gene counts for the relevant samples were downloaded and analysed using custom-made R scripts. Genes with low or no expression (cpm≥2 in at least three different sam-ples) were filtered and gene counts were normalised using the TMM method fromedgeR.
Normalised cpm were added with a pseudocount of 0.25 and then log2-transformed (log2(cpm)) and summarised over all samples. Gene lists were then grouped for GPCR class A and cAMP pathway-related signalling proteins according to Atwood and Mackie (2010) and median-ranked.
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